Prediction of auxin response elements based on data fusion in Arabidopsis thaliana

An Unexpected Regulatory Sequence from Rho-Related GTPase6 Confers Fiber-Specific Expression in Upland Cotton

Cotton fibers, single seed trichomes derived from ovule epidermal cells, are the major source of global textile fibers. Fiber-specific promoters are desirable to study gene function and to modify fiber properties during fiber development. Here, we revealed that Rho-related GTPase6 (GhROP6) was expressed preferentially in developing fibers. A 1240 bp regulatory region of GhROP6, which contains a short upstream regulatory sequence, the first exon, and the partial first intron, was unexpectedly isolated and introduced into transgenic cotton for analyzing promoter activity. The promoter of GhROP6 (proChROP6) conferred a specific expression in ovule surface, but not in the other floral organs and vegetative tissues. Reverse transcription PCR analysis indicated that proGhROP6 directed full-length transcription of the fused ß-glucuronidase (GUS) gene. Further investigation of GUS staining showed that proChROP6 regulated gene expression in fibers and ovule epidermis from fiber initiation to cell elongation stages. The preferential activity was enriched in fiber cells after anthesis and reached to peak on flowering days. By comparison, proGhROP6 was a mild promoter with approximately one-twenty-fifth of the strength of the constitutive promoter CaMV35S. The promoter responded to high-dosage treatments of auxin, gibberellin and salicylic acid and slightly reduced GUS activity under the in vitro treatment. Collectively, our data suggest that the GhROP6 promoter has excellent activity in initiating fibers and has potential for bioengineering of cotton fibers.

Auxin Directly Upregulates GhRAC13 Expression to Promote the Onset of Secondary Cell Wall Deposition in Cotton Fibers

Cotton fibers are single cells that show a relatively independent developmental process of cell differentiation, elongation, and secondary wall deposition. Auxin promotes fiber cell protrusion from the surface of the ovule. However, the role of auxin at other stages of cotton fiber development remains largely unknown. To gain a deeper insight into this aspect, we measured indoleacetic acid (IAA) content in developing fibers. Results showed an increase in IAA content at the transition stage from elongation to secondary cell wall deposition. Subsequently, we investigated the differences between two transgenic cottons that show upregulated and downregulated fiber auxin levels, respectively. In planta analysis revealed that, in addition to promoting cell elongation, auxin regulated the time of initiation of reactive oxygen species (ROS) production and secondary wall deposition in cotton fibers. This was closely correlated with the upregulated expression of GhRAC13, which regulates ROS-triggered cellulose synthesis. We found multiple putative auxin-responsive elements existed within the promoter region of GhRAC13, and IAA could induce proGhRAC13 activity. The dual-luciferase reporter assay further proved the activation of proGhRAC13 by GhARF5, an auxin-signaling activator. Altogether, our results suggest a role of auxin in promoting the onset of secondary growth by directly upregulating GhRAC13 expression in cotton fibers.

Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.)

Aux/IAA genes are early auxin-responsive genes and essential for auxin signaling transduction. There is little information about Aux/IAAs in the agriculturally important cereal, barley. Using in silico method, we identified and subsequently characterized 36 Aux/IAAs from the barley genome. Based on their genomic sequences and the phylogenic relationship with Arabidopsis and rice Aux/IAA, the 36 HvIAAs were categorized into two major groups and 14 subgroups. The indication of the presence or absence of these domains for the biological functions and acting mechanisms was discussed. The cis-element distributions in HvIAA promoters suggests that the HvIAAs expressions may not only regulated by auxin (the presence of AuxREs and TGA-element) but also by other hormones and developmental and environmental cues. We then studied the HvIAAs expression in response to NAA (1-Naphthaleneacetic acid) using quantitative real-time PCR (qRT-PCR). Like the promoter analysis, only 14 HvIAAs were upregulated by NAA over two-fold at 4 h. HvIAAs were clustered into three groups based on the spatiotemporal expression data. We confirmed by qRT-PCR that most HvIAAs, especially HvIAA3, HvIAA7, HvIAA8, HvIAA18, HvIAA24 and HvIAA34, are expressed in the developing barley spike compared within seedling, suggesting their roles in regulating spike development. Taken together, our data provide a foundation for further revealing the biological function of these HvIAAs.

Analysis of the impact of indole-3-acetic acid (IAA) on gene expression during leaf senescence in Arabidopsis thaliana

Leaf senescence is an important developmental process for the plant life cycle. It is controlled by endogenous and environmental factors and can be positively or negatively affected by plant growth regulators. It is characterised by major and significant changes in the patterns of gene expression. Auxin, especially indole-3-acetic acid (IAA), is a plant growth hormone that affects plant growth and development. The effect of IAA on leaf senescence is still unclear. In this study, we performed microarray analysis to investigate the role of IAA on gene expression during senescence in Arabidopsis thaliana. We sprayed IAA on plants at 3 different time points (27, 31 or 35 days after sowing). Following spraying, PSII activity of the eighth leaf was evaluated daily by measurement of chlorophyll fluorescence parameters. Our results show that PSII activity decreased following IAA application and the IAA treatment triggered different gene expression responses in leaves of different ages.

The roles of Aux/IAA gene family in development of Dendrocalamus sinicus (Poaceae: Bambusoideae) inferred by comprehensive analysis and expression profiling

Auxin is an important hormone in many plant developmental processes. In this study, the auxin/indole acetic acid (Aux/IAA) gene family was comprehensively identified using Dendrocalamus sinicus transcriptome data. A total of 26 Aux/IAA genes (DsIAA1-DsIAA26) were mined using four conserved Aux/IAA family motifs (PF02309). They encoded hydrophilic proteins, including one or two nuclear localisation signals. The D. sinicus Aux/IAA proteins were classified into two groups, including seven sister-gene pairs based on their phylogenetic relationships. A phylogenetic tree generated by aligning 108 predicted protein sequences of 26 DsIAAs, 43 PhIAAs (Phyllostachys heterocycla), 29 AtIAAs (Arabidopsis), 31 OsIAAs (Oryza sativa) and 22 PtIAAs (Populus) revealed nine major groups. Among them, four groups, including 96 IAA proteins of all five species, suggested that the genes originated before divergence of monocots and dicots. The expression profiling in different tissues showed that most of the DsIAAs preferentially expressed in leaves and shoots, suggesting their important roles in the development of leaves and shoots in D. sinicus. Continuously high expression of DsIAA3, DsIAA4, DsIAA15, and DsIAA20 may be important for regulating shoot development in D. sinicus. These results provide useful information for further research into the function of Aux/IAA genes in woody sympodial bamboos.